LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 3
  using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units        electron
dimension    3
boundary     p p p
atom_style   atomic
atom_modify  map yes
pair_style   none

# Time step (in femtoseconds)
timestep     0.5

# Temperature (in Kelvin)
variable     Temp equal 17.4

# Number of Nose-Hoover chains
variable     nhc equal 4

# Force constant (in Hartree energies per Bohr radius squared)
variable     k equal 1.2154614120000001e-08

# Number of beads
variable     Nbeads equal 4
variable     ibead uloop ${Nbeads} pad
variable     ibead uloop 4 pad
variable     seed equal 18889

# Create box and atoms. All distances are in Bohr
region       box block -1500 1500 -1500 1500 -1500 1500
create_box   1 box
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
  1 by 1 by 1 MPI processor grid
variable     a loop 3
label        loop
variable     x1 equal -15.0+0.5*v_a
variable     y1 equal 10.0-0.5*v_a
variable     z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14.5 ${y1} ${z1}
create_atoms 1 single -14.5 9.5 ${z1}
create_atoms 1 single -14.5 9.5 1.5
Created 1 atoms
  using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
  create_atoms CPU = 0.000 seconds
next         a
jump         SELF loop
variable     x1 equal -15.0+0.5*v_a
variable     y1 equal 10.0-0.5*v_a
variable     z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14 ${y1} ${z1}
create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2
Created 1 atoms
  using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
  create_atoms CPU = 0.000 seconds
next         a
jump         SELF loop
variable     x1 equal -15.0+0.5*v_a
variable     y1 equal 10.0-0.5*v_a
variable     z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -13.5 ${y1} ${z1}
create_atoms 1 single -13.5 8.5 ${z1}
create_atoms 1 single -13.5 8.5 2.5
Created 1 atoms
  using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
  create_atoms CPU = 0.000 seconds
next         a
jump         SELF loop

# Electron mass (in amu)
mass         1 0.00054858

# Initialize velocities
velocity     all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
velocity     all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
velocity     all create 17.4 18889${ibead} mom yes rot yes dist gaussian
velocity     all create 17.4 188894 mom yes rot yes dist gaussian

# Add harmonic external force
fix          harm all spring/self ${k}
fix          harm all spring/self 1.215461412e-08

# Add harmonic potential energy to total energy and potential energy
fix_modify   harm energy yes

# PIMD command
fix          pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc}
fix          pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc}
fix          pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4

# Outputs
variable virial        equal f_pimdb[3]
variable prim_kinetic  equal f_pimdb[4]

thermo_style custom step pe v_virial v_prim_kinetic
thermo          1

run             100
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
   Step         PotEng        v_virial    v_prim_kinetic
         0   0              0              0.00024796164
         1   8.5847879e-10  4.4463719e-10  0.00024796024
         2   3.4336684e-09  1.3183829e-09  0.00024795602
         3   7.7250055e-09  2.6210625e-09  0.000247949  
         4   1.3731669e-08  4.3524371e-09  0.00024793917
         5   2.1452581e-08  6.5122035e-09  0.00024792653
         6   3.0886407e-08  9.0999942e-09  0.0002479111 
         7   4.2031554e-08  1.2115377e-08  0.00024789287
         8   5.4886174e-08  1.5557858e-08  0.00024787185
         9   6.9448162e-08  1.9426875e-08  0.00024784804
        10   8.5715159e-08  2.3721806e-08  0.00024782146
        11   1.0368455e-07  2.8441963e-08  0.0002477921 
        12   1.2335346e-07  3.3586595e-08  0.00024775998
        13   1.4471878e-07  3.9154888e-08  0.0002477251 
        14   1.6777712e-07  4.5145965e-08  0.00024768748
        15   1.9252485e-07  5.1558884e-08  0.00024764712
        16   2.1895809e-07  5.8392642e-08  0.00024760403
        17   2.4707272e-07  6.5646173e-08  0.00024755823
        18   2.7686434e-07  7.3318348e-08  0.00024750973
        19   3.0832834e-07  8.1407976e-08  0.00024745854
        20   3.4145982e-07  8.9913804e-08  0.00024740467
        21   3.7625367e-07  9.8834518e-08  0.00024734813
        22   4.127045e-07   1.0816874e-07  0.00024728895
        23   4.5080671e-07  1.1791504e-07  0.00024722714
        24   4.9055443e-07  1.2807191e-07  0.00024716271
        25   5.3194155e-07  1.3863779e-07  0.00024709568
        26   5.7496174e-07  1.4961107e-07  0.00024702607
        27   6.1960841e-07  1.6099007e-07  0.00024695389
        28   6.6587473e-07  1.7277305e-07  0.00024687917
        29   7.1375365e-07  1.8495821e-07  0.00024680191
        30   7.6323786e-07  1.975437e-07   0.00024672216
        31   8.1431984e-07  2.1052759e-07  0.00024663991
        32   8.6699183e-07  2.2390793e-07  0.0002465552 
        33   9.2124582e-07  2.3768267e-07  0.00024646805
        34   9.7707361e-07  2.5184974e-07  0.00024637847
        35   1.0344667e-06  2.6640698e-07  0.0002462865 
        36   1.0934165e-06  2.813522e-07   0.00024619215
        37   1.1539141e-06  2.9668313e-07  0.00024609545
        38   1.2159503e-06  3.1239747e-07  0.00024599643
        39   1.2795157e-06  3.2849286e-07  0.00024589511
        40   1.344601e-06   3.4496686e-07  0.00024579151
        41   1.4111961e-06  3.61817e-07    0.00024568566
        42   1.4792913e-06  3.7904076e-07  0.0002455776 
        43   1.5488762e-06  3.9663555e-07  0.00024546734
        44   1.6199404e-06  4.1459874e-07  0.00024535492
        45   1.6924734e-06  4.3292764e-07  0.00024524035
        46   1.7664643e-06  4.5161952e-07  0.00024512369
        47   1.841902e-06   4.7067159e-07  0.00024500494
        48   1.9187753e-06  4.90081e-07    0.00024488415
        49   1.9970729e-06  5.0984488e-07  0.00024476135
        50   2.076783e-06   5.2996028e-07  0.00024463656
        51   2.1578939e-06  5.5042422e-07  0.00024450981
        52   2.2403935e-06  5.7123366e-07  0.00024438115
        53   2.3242696e-06  5.9238553e-07  0.0002442506 
        54   2.4095099e-06  6.138767e-07   0.00024411819
        55   2.4961017e-06  6.3570399e-07  0.00024398396
        56   2.5840323e-06  6.5786419e-07  0.00024384795
        57   2.6732887e-06  6.8035404e-07  0.00024371018
        58   2.7638579e-06  7.0317021e-07  0.0002435707 
        59   2.8557265e-06  7.2630938e-07  0.00024342953
        60   2.9488811e-06  7.4976814e-07  0.00024328672
        61   3.0433081e-06  7.7354305e-07  0.0002431423 
        62   3.1389936e-06  7.9763065e-07  0.00024299631
        63   3.2359238e-06  8.2202741e-07  0.00024284878
        64   3.3340844e-06  8.4672977e-07  0.00024269976
        65   3.4334612e-06  8.7173415e-07  0.00024254927
        66   3.5340397e-06  8.970369e-07   0.00024239736
        67   3.6358055e-06  9.2263435e-07  0.00024224406
        68   3.7387437e-06  9.4852279e-07  0.00024208942
        69   3.8428394e-06  9.7469849e-07  0.00024193348
        70   3.9480777e-06  1.0011576e-06  0.00024177626
        71   4.0544433e-06  1.0278964e-06  0.00024161782
        72   4.1619211e-06  1.054911e-06   0.0002414582 
        73   4.2704954e-06  1.0821976e-06  0.00024129742
        74   4.3801508e-06  1.1097521e-06  0.00024113554
        75   4.4908716e-06  1.1375706e-06  0.0002409726 
        76   4.6026419e-06  1.1656492e-06  0.00024080863
        77   4.7154459e-06  1.1939839e-06  0.00024064367
        78   4.8292673e-06  1.2225706e-06  0.00024047778
        79   4.9440901e-06  1.2514052e-06  0.00024031099
        80   5.059898e-06   1.2804837e-06  0.00024014333
        81   5.1766745e-06  1.309802e-06   0.00023997487
        82   5.2944032e-06  1.3393558e-06  0.00023980562
        83   5.4130674e-06  1.369141e-06   0.00023963565
        84   5.5326505e-06  1.3991534e-06  0.00023946499
        85   5.6531355e-06  1.4293887e-06  0.00023929369
        86   5.7745057e-06  1.4598429e-06  0.00023912178
        87   5.8967439e-06  1.4905114e-06  0.00023894931
        88   6.0198332e-06  1.5213902e-06  0.00023877633
        89   6.1437564e-06  1.5524748e-06  0.00023860287
        90   6.2684962e-06  1.5837609e-06  0.00023842898
        91   6.3940353e-06  1.6152441e-06  0.00023825471
        92   6.5203562e-06  1.6469202e-06  0.0002380801 
        93   6.6474416e-06  1.6787847e-06  0.00023790518
        94   6.7752739e-06  1.7108332e-06  0.00023773001
        95   6.9038354e-06  1.7430613e-06  0.00023755463
        96   7.0331085e-06  1.7754645e-06  0.00023737908
        97   7.1630755e-06  1.8080385e-06  0.00023720341
        98   7.2937187e-06  1.8407787e-06  0.00023702765
        99   7.4250201e-06  1.8736806e-06  0.00023685186
       100   7.5569619e-06  1.9067398e-06  0.00023667607
Loop time of 0.00197094 on 1 procs for 100 steps with 3 atoms

Performance: 2191851993.165 fs/day, 0.000 hours/fs, 50737.315 timesteps/s, 152.212 katom-step/s
37.5% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Neigh   | 1.652e-06  | 1.652e-06  | 1.652e-06  |   0.0 |  0.08
Comm    | 1.7965e-05 | 1.7965e-05 | 1.7965e-05 |   0.0 |  0.91
Output  | 0.00036011 | 0.00036011 | 0.00036011 |   0.0 | 18.27
Modify  | 0.0015231  | 0.0015231  | 0.0015231  |   0.0 | 77.28
Other   |            | 6.806e-05  |            |       |  3.45

Nlocal:              3 ave           3 max           3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 24
Dangerous builds = 0
Total wall time: 0:00:00
